Installation of pygetpapers and ami3 on MacOS (Intel-based)

Maintained by: Ankit Lade

System specifications :

• MacBook Air (13-inch, 2017)
• Processor: 1.8 GHz Dual-Core Intel Core i5
• Software: macOS Big Sur version 11.5.2

Date: 15/09/2021

Pre-requisite

A system must have Python and pip packages installed on the system. MacOS comes with default Python2.7, but we'll use Python3 in most of the cases. First, check if Python3 is installed on the system or not by python --version this command. If it gives Python2 version try checking using python3 --version. If the Python3 version is not installed please follow these steps to install it on your system.

1. Open the terminal and install Homebrew using the following code.

/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install.sh)"

2. Now install the latest version of Python3 using the brew install python3 command.

3. After installing check your version by the python --version or python3 --version command.

Check if pip is installed on the system or not by running either of these commands pip --version or pip3 --version. If pip is not installed then follow the steps given below.

1. Use the following command to download pip directly,

curl https://bootstrap.pypa.io/get-pip.py -o get-pip.py

2. Now execute the downloaded file using the command

python3 get-pip.py

and wait through the installation process.

3. After installing check your version by the pip --version or pip3 --version command.

Check if git is installed on the system or not by running either of these commands git --version. If pip is not installed then follow the steps given below.

1. Download git for your system from https://git-scm.com/downloads

2. Install the package and check if git is successfully installed by running git -version on the terminal.

pygetpapers

We install pygetpapers using pip command. It is a useful tool inspired by getpapers and helps in downloading full scientific research papers available on the EUPMC repository.

Installing pygetpapers

1. Run the command

pip install pygetpapers

2. Check if your installation was successful by typing pygetpapers --help. This command opens the pygetpapers help prompt on terminal.

For More Details on pygetpapers visit: https://github.com/petermr/pygetpapers

Installing ami3

ami3 is a toolkit to manage (scholarly) documents; download, aggregate, transform, search, filter, index, annotate, re-use and republish. ami3 is written in Java, and is designed to be a declarative system, with commands and data modules. Since ami3 is written in Java we will install Java and Java development kit.

Installing Java and jdk

To download the latest version of Java on the macOS system visit this: https://www.java.com/en/download/. it will download a .dmg package that you'll install on your system. Once the installation is complete test if the installation was successful by typing java -version in the terminal.

To download latest JDK on the system visit this: https://www.oracle.com/java/technologies/javase-jdk16-downloads.html

Install the downloaded package and after installation check JDK version by running following command on the terminal.

ls /Library/Java/JavaVirtualMachines

Install Maven

Download the maven package for your system from https://maven.apache.org/download.cgi. Download apache-maven-3.8.2-bin.zip (version may differ but download the one having .zip extension) from this link. Move this to the Applications folder and unzip the apache-maven-3.8.2-bin.zip file using the following command.

mv ~/Downloads/apache-maven-3.8.2-bin.zip ~/Applications/apache-maven-3.8.2-bin
unzip apache-maven-3.8.2-bin

Now set the path for maven: -> Open bash profile by open -e .bash_profile in the home directory(to go to the home directory run cd in the terminal). This will open a text edit file.

-> If the bash profile is not present in the directory, create it using touch .bash_profile and then open the bash profile using the open -e .bash_profile command.

-> Press enter to go to new line and edit the text file by pasting this in the file :

export M2_HOME=/Users/ankitlade/Applications/apache-maven-3.8.2
export PATH=$PATH:$M2_HOME/bin

-> Save the file and close it.

-> Run the following command on the terminal.

source .bash_profile

-> Install maven by

mvn -install

You can also follow this youtube link for maven installation: https://youtu.be/j0OnSAP-KtU

Check the maven installation by typing mvn -version on the command line, it should show apache-maven-3.8.2 (The version may differ in the future).

ami3

Clone the ami3 repository on the system from the terminal using the following command

git clone https://github.com/petermr/ami3.git

Move the ami3 folder from the home directory to the /Applications directory using the following command

mv ~/ami3 ~/Applications/ami3/

Set the path for ami3, open bash profile by open -e .bash_profile and add the following lines :

export A2_HOME=/Users/ankitlade/Applications/ami3/target/appassembler
export PATH=$PATH:$A2_HOME/bin

Save and close the bash profile.

On the terminal change directory :

cd Applications/ami3

Run the following command, it will take some time for installation.

mvn install -Dmaven.test.skip=true

Restart your terminal and check ami3 installation by typing ami --help. It will open the help message if ami is installed properly.